python-biopython

maintainer kbipinkumar · 1 votes · scanned 2026-08-03 00:08:14.047287

LOW

Why flagged The source is a tarball from the project's official domain (biopython.org), which is plausibly the project's own release infrastructure; building from official project sources is normal for AUR packages, even if the host is not on a whitelist.

Triggered rules

LOW AI review downgraded a static finding llm_review

The static rules flagged this MEDIUM, but an AI model (qwen/qwen3-235b-a22b-07-25) reviewed the full PKGBUILD and judged it LOW (confidence 95%): The source is a tarball from the project's official domain (biopython.org), which is plausibly the project's own release infrastructure; building from official project sources is normal for AUR packages, even if the host is not on a whitelist.

1 higher static finding superseded - not the current verdict (shown for transparency)

MEDIUM source=() URL on a non-standard host source_untrusted_domain

One or more source=() URLs point to a host outside the trusted allowlist (github.com, gitlab.com, codeberg.org, pypi.org, …).

PKGBUILD:24 source=("http://www.biopython.org/DIST/${_pkgname}-${pkgver}.tar.gz"

PKGBUILD

1 offending line(s) highlighted

      1# Maintainer: Bipin Kumar <kbipinkumar@pm.me>
    
      2# Contributor: Evgeniy Alekseev <arcanis.arch at gmail dot com>
    
      3# Contributor: Stunts <f.pinamartins at gmail dot com>
    
      4# Contributor: damir <damir at archlinux dot org>
    
      5
    
      6pkgname=python-biopython
    
      7_pkgname=biopython
    
      8pkgver=1.87
    
      9pkgrel=1
    
      10pkgdesc="Freely available Python tools for computational molecular biology"
    
      11arch=('x86_64')
    
      12url="http://www.biopython.org"
    
      13license=('LicenseRef-Biopython License')
    
      14makedepends=('python-setuptools' 'python-build' 'python-installer' 'python-wheel')
    
      15checkdepends=('python-scipy' 'python-rdflib' 'python-igraph' 'python-reportlab' 'python-networkx' 'python-mmtf' 'python-matplotlib' 'python-coverage')
    
      16depends=('python-numpy' 'glibc' 'python' 'python-scipy' 'python-pillow')
    
      17# optdepends from https://github.com/biopython/biopython?tab=readme-ov-file#optional-dependencies
    
      18optdepends=('python-mysql-connector: for BioSQL module'
    
      19            'python-reportlab: for graph generation'
    
      20            'python-networkx: for certain niche functions in Bio.Phylo module'
    
      21            'python-matplotlib: to plot phylogenetic trees.'
    
      22            'python-rdflib: CDAO parser under Bio.Phylo module'
    
      23           )
    
      24source=("http://www.biopython.org/DIST/${_pkgname}-${pkgver}.tar.gz"
    
      25       )
    
      26sha512sums=('aed9131f85b28d1b6fb7b1878d6afe2b701eddae092514ec43c69b623c871e16dbf5aaed464709423031169c0c13709bfbc0055e4cdc89c766e4445b959ba7a5')
    
      27options=(!debug)
    
      28
    
      29build() {
    
      30  cd "${srcdir}/${_pkgname}-${pkgver}"
    
      31  python -m build --wheel --no-isolation
    
      32}
    
      33
    
      34check() {
    
      35  local pyver=$(python -c 'import sys; print(*sys.version_info[:2], sep="")')
    
      36  cd "${srcdir}/${_pkgname}-${pkgver}"
    
      37  PYTHONPATH="$PWD/build/lib.linux-${CARCH}-cpython-${pyver}" python Tests/run_tests.py --offline
    
      38}
    
      39
    
      40package() {
    
      41  cd "${srcdir}/${_pkgname}-${pkgver}"
    
      42  python -m installer --destdir="${pkgdir}" dist/*.whl
    
      43  install -Dm644 "LICENSE.rst" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
    
      44}
    
      45

Scan history

Scanned at (UTC)	Severity	Rules
2026-08-03 00:08:14	LOW	2
2026-08-02 00:16:08	LOW	2
2026-08-01 00:11:18	LOW	2
2026-07-31 00:14:10	LOW	2
2026-07-30 00:17:23	LOW	2
2026-07-29 00:25:53	LOW	2
2026-07-28 00:07:28	LOW	2
2026-07-27 00:24:32	LOW	2
2026-07-26 00:07:32	LOW	2
2026-07-25 00:13:44	LOW	2
2026-07-24 00:02:28	LOW	2
2026-07-23 00:14:47	LOW	2
2026-07-22 00:29:32	LOW	2
2026-07-21 00:24:15	LOW	2
2026-07-20 00:19:49	LOW	2
2026-07-19 00:17:08	LOW	2
2026-07-18 00:14:48	LOW	2
2026-07-17 00:06:16	LOW	2
2026-07-16 00:05:41	LOW	2
2026-07-15 00:09:25	LOW	2